[AMBER] AmberTools14 MMPBSA CalcError with complex.prmtop and SA Bomb in use_sander=1

From: Kenneth Huang <kennethneltharion.gmail.com>
Date: Mon, 12 Jan 2015 14:45:52 -0500

Dear all,

I'm running into a frankly bizarre error with MMPBSA using AmberTools14.
After generating my complex/ligand/receptor prmtop files with ante-MMPBSA
using this command-

ante-MMPBSA.py -p sol.prmtop -c com.prmtop -r rec.prmtop -l lig.prmtop -s
':WAT,:Na+' -n ':1-521,:1562-2082'

I then tried testing a short, two frame test run in MMPBSA with my input as-

   startframe=269, endframe=270, interval=1, keep_files=2,
receptor_mask=':522-1561:2083-2084', ligand_mask=':1-521:1562-2082',
  radiopt=0, indi=2.0,

Which then proceeded to crash with a CalcError failure with the complex.
The log showed that it was crashing at GB calculations, but checking
_MMPBSA_complex_gb.mdout.0 only provided this-

Processing ASCII trajectory (_MMPBSA_complex.mdcrd.0)

Processing frame 1
      iter Total bad vdW elect nonpolar genBorn

So trying to see what exactly was causing the crash, I ran MMPBSA with
use_sander=1 in the input. Strangely enough, the log file/outputs show it
crashing with the same complex CalcError at PB instead of GB.
_MMPBSA_complex_gb.mdout.0 is actually completing, or doing a very good job
of looking as if it's successful- but checking _MMPBSA_complex_pb.mdout.0
gives me this message-

Cpptraj Generated trajectory

minimizing coord set # 1
SA Bomb in sa_arc(): Allocates aborted 3 0 5014 5014 0 0

I figured I'd try running mmpbsa_py_energy to see if I couldn't get a more
clear idea of what the error was, but oddly enough running _MMPBSA_pb.mdin
and _MMPBSA_gb.mdin with mmpbsa_py_energy both seem to complete without a

 BOND = 6139.4423 ANGLE = 16044.7359 DIHED =
 VDWAALS = -16859.4284 EEL = -151313.2641 EGB =
 1-4 VDW = 7348.3643 1-4 EEL = 82548.4930 RESTRAINT =
 ESURF = 590.8814

MM/GBSA processing done!

 BOND = 6139.4423 ANGLE = 16044.7359 DIHED =
 VDWAALS = -16859.4284 EEL = -75656.6320 EPB =
 1-4 VDW = 7348.3643 1-4 EEL = 82548.4930 RESTRAINT =
 ECAVITY = 15063.6475 EDISPER = -7396.2674
MM/PBSA processing done!

 Total surface charge 7.9234
 Reaction field energy -10359.5105
 Cavity solvation energy 15063.6475
 Dispersion solvation energy -7396.2674

I've tried running MMPBSA on a slightly different system that
also uses requisite prmtop files using the same command for ante-MMPBSA,
and the behavior is exactly the same. Yet when I run MMPBSA on a different
system that uses prmtop files that I haven't made using ante-MMPBSA, it's
able to run without a problem.

At this point, I'm not really sure what to make of this error- I was
initially thinking it might've been a problem with my mask selection for
the ligand/receptor, but that mmpbsa_py_energy is actually able to give
outputs has me wondering if there's something wrong with how I made the
prmtops with ante-MMPBSA, or something else is going on entirely.


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Received on Mon Jan 12 2015 - 12:00:04 PST
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